TRUA_ECOLI
ID TRUA_ECOLI Reviewed; 270 AA.
AC P07649;
DT 01-APR-1988, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1988, sequence version 1.
DT 03-AUG-2022, entry version 179.
DE RecName: Full=tRNA pseudouridine synthase A;
DE EC=5.4.99.12;
DE AltName: Full=tRNA pseudouridine(38-40) synthase;
DE AltName: Full=tRNA pseudouridylate synthase I;
DE Short=PSU-I;
DE AltName: Full=tRNA-uridine isomerase I;
GN Name=truA; Synonyms=asuC, hisT, leuK; OrderedLocusNames=b2318, JW2315;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=2991861; DOI=10.1093/nar/13.14.5297;
RA Arps P.J., Marvel C.C., Rubin B.C., Tolan D.A., Penhoet E.E., Winkler M.E.;
RT "Structural features of the hisT operon of Escherichia coli K-12.";
RL Nucleic Acids Res. 13:5297-5315(1985).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 255-270.
RC STRAIN=K12;
RX PubMed=3040734; DOI=10.1016/s0021-9258(18)45338-0;
RA Nonet M.L., Marvel C.C., Tolan D.R.;
RT "The hisT-purF region of the Escherichia coli K-12 chromosome.
RT Identification of additional genes of the hisT and purF operons.";
RL J. Biol. Chem. 262:12209-12217(1987).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-10 AND 267-270.
RC STRAIN=K12;
RX PubMed=3029016; DOI=10.1128/jb.169.3.1061-1070.1987;
RA Arps P.J., Winkler M.E.;
RT "Structural analysis of the Escherichia coli K-12 hisT operon by using a
RT kanamycin resistance cassette.";
RL J. Bacteriol. 169:1061-1070(1987).
RN [7]
RP PROTEIN SEQUENCE, AND CHARACTERIZATION.
RX PubMed=3276686; DOI=10.1016/s0021-9258(18)69199-9;
RA Kammen H.O., Marvel C.C., Hardy L., Penhoet E.E.;
RT "Purification, structure, and properties of Escherichia coli tRNA
RT pseudouridine synthase I.";
RL J. Biol. Chem. 263:2255-2263(1988).
RN [8]
RP ACTIVE SITE.
RX PubMed=9425056; DOI=10.1021/bi971874+;
RA Huang L., Pookanjanatavip M., Gu X., Santi D.V.;
RT "A conserved aspartate of tRNA pseudouridine synthase is essential for
RT activity and a probable nucleophilic catalyst.";
RL Biochemistry 37:344-351(1998).
RN [9]
RP ACTIVE SITE.
RX PubMed=10588695; DOI=10.1073/pnas.96.25.14270;
RA Gu X., Liu Y., Santi D.V.;
RT "The mechanism of pseudouridine synthase I as deduced from its interaction
RT with 5-fluorouracil-tRNA.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:14270-14275(1999).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 7-270, AND SUBUNIT.
RX PubMed=10625422; DOI=10.1038/71219;
RA Foster P.G., Huang L., Santi D.V., Stroud R.M.;
RT "The structural basis for tRNA recognition and pseudouridine formation by
RT pseudouridine synthase I.";
RL Nat. Struct. Biol. 7:23-27(2000).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (3.9 ANGSTROMS) OF 7-270 IN COMPLEX WITH TRNA,
RP CATALYTIC ACTIVITY, FUNCTION, SUBUNIT, AND MUTAGENESIS OF ARG-58.
RX PubMed=17466622; DOI=10.1016/j.molcel.2007.02.027;
RA Hur S., Stroud R.M.;
RT "How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation
RT by TruA.";
RL Mol. Cell 26:189-203(2007).
CC -!- FUNCTION: Formation of pseudouridine at positions 38, 39 and 40 in the
CC anticodon stem and loop of transfer RNAs.
CC {ECO:0000269|PubMed:17466622}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA;
CC Xref=Rhea:RHEA:22376, Rhea:RHEA-COMP:10085, Rhea:RHEA-COMP:10087,
CC ChEBI:CHEBI:65314, ChEBI:CHEBI:65315; EC=5.4.99.12;
CC Evidence={ECO:0000269|PubMed:17466622};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10625422,
CC ECO:0000269|PubMed:17466622}.
CC -!- SIMILARITY: Belongs to the tRNA pseudouridine synthase TruA family.
CC {ECO:0000305}.
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DR EMBL; X02743; CAA26522.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75378.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16175.1; -; Genomic_DNA.
DR EMBL; M68934; AAA23963.1; -; Genomic_DNA.
DR EMBL; M15542; AAA24313.1; -; Genomic_DNA.
DR EMBL; M15543; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; B23792; SYECZ1.
DR RefSeq; NP_416821.1; NC_000913.3.
DR RefSeq; WP_001283586.1; NZ_LN832404.1.
DR PDB; 1DJ0; X-ray; 1.50 A; A/B=7-270.
DR PDB; 2NQP; X-ray; 3.50 A; A/B/C/D=1-270.
DR PDB; 2NR0; X-ray; 3.90 A; A/B/C/D=1-270.
DR PDB; 2NRE; X-ray; 4.00 A; A=1-270.
DR PDBsum; 1DJ0; -.
DR PDBsum; 2NQP; -.
DR PDBsum; 2NR0; -.
DR PDBsum; 2NRE; -.
DR AlphaFoldDB; P07649; -.
DR SMR; P07649; -.
DR BioGRID; 4261359; 63.
DR BioGRID; 851134; 4.
DR DIP; DIP-11043N; -.
DR IntAct; P07649; 9.
DR STRING; 511145.b2318; -.
DR jPOST; P07649; -.
DR PaxDb; P07649; -.
DR PRIDE; P07649; -.
DR EnsemblBacteria; AAC75378; AAC75378; b2318.
DR EnsemblBacteria; BAA16175; BAA16175; BAA16175.
DR GeneID; 946793; -.
DR KEGG; ecj:JW2315; -.
DR KEGG; eco:b2318; -.
DR PATRIC; fig|1411691.4.peg.4416; -.
DR EchoBASE; EB0449; -.
DR eggNOG; COG0101; Bacteria.
DR HOGENOM; CLU_014673_0_2_6; -.
DR InParanoid; P07649; -.
DR OMA; FLYGMVR; -.
DR PhylomeDB; P07649; -.
DR BioCyc; EcoCyc:EG10454-MON; -.
DR BioCyc; MetaCyc:EG10454-MON; -.
DR EvolutionaryTrace; P07649; -.
DR PRO; PR:P07649; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0009982; F:pseudouridine synthase activity; IBA:GO_Central.
DR GO; GO:0000049; F:tRNA binding; IDA:EcoCyc.
DR GO; GO:0106029; F:tRNA pseudouridine synthase activity; IDA:EcoCyc.
DR GO; GO:0031119; P:tRNA pseudouridine synthesis; IMP:EcoCyc.
DR CDD; cd02570; PseudoU_synth_EcTruA; 1.
DR Gene3D; 3.30.70.580; -; 1.
DR Gene3D; 3.30.70.660; -; 1.
DR HAMAP; MF_00171; TruA; 1.
DR InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR InterPro; IPR001406; PsdUridine_synth_TruA.
DR InterPro; IPR020097; PsdUridine_synth_TruA_a/b_dom.
DR InterPro; IPR020095; PsdUridine_synth_TruA_C.
DR InterPro; IPR020094; TruA/RsuA/RluB/E/F_N.
DR PANTHER; PTHR11142; PTHR11142; 1.
DR Pfam; PF01416; PseudoU_synth_1; 2.
DR PIRSF; PIRSF001430; tRNA_psdUrid_synth; 1.
DR SUPFAM; SSF55120; SSF55120; 1.
DR TIGRFAMs; TIGR00071; hisT_truA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Isomerase; Reference proteome;
KW tRNA processing.
FT CHAIN 1..270
FT /note="tRNA pseudouridine synthase A"
FT /id="PRO_0000057375"
FT REGION 107..111
FT /note="RNA binding"
FT REGION 168..172
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000269|PubMed:17466622"
FT ACT_SITE 60
FT /note="Nucleophile"
FT /evidence="ECO:0000269|PubMed:10588695,
FT ECO:0000269|PubMed:9425056"
FT BINDING 118
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17466622"
FT SITE 58
FT /note="Interaction with tRNA; Important for base-flipping"
FT /evidence="ECO:0000269|PubMed:17466622"
FT SITE 78
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000269|PubMed:17466622"
FT SITE 110
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000269|PubMed:17466622"
FT SITE 126
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000269|PubMed:17466622"
FT SITE 139
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000269|PubMed:17466622"
FT MUTAGEN 58
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:17466622"
FT STRAND 10..18
FT /evidence="ECO:0007829|PDB:1DJ0"
FT HELIX 20..22
FT /evidence="ECO:0007829|PDB:2NQP"
FT STRAND 30..32
FT /evidence="ECO:0007829|PDB:2NQP"
FT HELIX 35..47
FT /evidence="ECO:0007829|PDB:1DJ0"
FT STRAND 53..57
FT /evidence="ECO:0007829|PDB:1DJ0"
FT STRAND 64..75
FT /evidence="ECO:0007829|PDB:1DJ0"
FT HELIX 80..89
FT /evidence="ECO:0007829|PDB:1DJ0"
FT STRAND 95..102
FT /evidence="ECO:0007829|PDB:1DJ0"
FT TURN 109..112
FT /evidence="ECO:0007829|PDB:1DJ0"
FT STRAND 115..123
FT /evidence="ECO:0007829|PDB:1DJ0"
FT STRAND 125..127
FT /evidence="ECO:0007829|PDB:1DJ0"
FT TURN 131..134
FT /evidence="ECO:0007829|PDB:1DJ0"
FT STRAND 135..138
FT /evidence="ECO:0007829|PDB:1DJ0"
FT HELIX 145..152
FT /evidence="ECO:0007829|PDB:1DJ0"
FT HELIX 153..155
FT /evidence="ECO:0007829|PDB:1DJ0"
FT STRAND 157..160
FT /evidence="ECO:0007829|PDB:1DJ0"
FT HELIX 162..164
FT /evidence="ECO:0007829|PDB:1DJ0"
FT STRAND 175..186
FT /evidence="ECO:0007829|PDB:1DJ0"
FT STRAND 189..197
FT /evidence="ECO:0007829|PDB:1DJ0"
FT HELIX 203..215
FT /evidence="ECO:0007829|PDB:1DJ0"
FT HELIX 223..230
FT /evidence="ECO:0007829|PDB:1DJ0"
FT HELIX 233..235
FT /evidence="ECO:0007829|PDB:1DJ0"
FT STRAND 245..251
FT /evidence="ECO:0007829|PDB:1DJ0"
FT HELIX 254..256
FT /evidence="ECO:0007829|PDB:1DJ0"
SQ SEQUENCE 270 AA; 30400 MW; 8E97BC88C3220188 CRC64;
MSDQQQPPVY KIALGIEYDG SKYYGWQRQN EVRSVQEKLE KALSQVANEP ITVFCAGRTD
AGVHGTGQVV HFETTALRKD AAWTLGVNAN LPGDIAVRWV KTVPDDFHAR FSATARRYRY
IIYNHRLRPA VLSKGVTHFY EPLDAERMHR AAQCLLGEND FTSFRAVQCQ SRTPWRNVMH
INVTRHGPYV VVDIKANAFV HHMVRNIVGS LMEVGAHNQP ESWIAELLAA KDRTLAAATA
KAEGLYLVAV DYPDRYDLPK PPMGPLFLAD
